PDBsum entry 3d4f

Hydrolase

PDB id: 3d4f

Contents

Protein chain

265 a.a. *

Ligands

MA4 ×2

LN1

Waters ×248

* Residue conservation analysis

PDB id:

3d4f

Name:

Hydrolase

Title:

Shv-1 beta-lactamase complex with ln1-255

Structure:

Beta-lactamase shv-1. Chain: a. Synonym: pit-2. Engineered: yes

Source:

Klebsiella pneumoniae. Organism_taxid: 573. Gene: bla, shv1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.55Å R-factor: 0.168 R-free: 0.197

Authors:

P.Pattanaik,C.R.Bethel,A.M.Hujer,R.A.Bonomo,J.D.Buynak,F.Van Den Akker

Key ref:

P.Pattanaik et al. (2009). Strategic Design of an Effective {beta}-Lactamase Inhibitor: LN-1-255, A 6-ALKYLIDENE-2'-SUBSTITUTED PENICILLIN SULFONE. J Biol Chem, 284, 945-953. PubMed id: 18955486 DOI: 10.1074/jbc.M806833200

Date:

14-May-08 Release date: 10-Feb-09

Protein chain

P0AD64  (BLA1_KLEPN) -  Beta-lactamase SHV-1 from Klebsiella pneumoniae

Seq: 286 a.a.

Struc: 265 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.2.6 - beta-lactamase.
• Pathway: Penicillin Biosynthesis and Metabolism
• Reaction: a beta-lactam + H2O = a substituted beta-amino acid
• Cofactor: Zn(2+)

DOI no: 10.1074/jbc.M806833200

J Biol Chem 284:945-953 (2009)

PubMed id: 18955486

Strategic Design of an Effective {beta}-Lactamase Inhibitor: LN-1-255, A 6-ALKYLIDENE-2'-SUBSTITUTED PENICILLIN SULFONE.

P.Pattanaik, C.R.Bethel, A.M.Hujer, K.M.Hujer, A.M.Distler, M.Taracila, V.E.Anderson, T.R.Fritsche, R.N.Jones, S.R.Pagadala, F.van den Akker, J.D.Buynak, R.A.Bonomo.

ABSTRACT

In an effort to devise strategies for overcoming bacterial beta-lactamases, we studied LN-1-255, a 6-alkylidene-2'-substituted penicillin sulfone inhibitor. By possessing a catecholic functionality that resembles a natural bacterial siderophore, LN-1-255 is unique among beta-lactamase inhibitors. LN-1-255 combined with piperacillin was more potent against Escherichia coli DH10B strains bearing bla(SHV) extended-spectrum and inhibitor-resistant beta-lactamases than an equivalent amount of tazobactam and piperacillin. In addition, LN-1-255 significantly enhanced the activity of ceftazidime and cefpirome against extended-spectrum cephalosporin and Sme-1 containing carbapenem-resistant clinical strains. LN-1-255 inhibited SHV-1 and SHV-2 beta-lactamases with nm affinity (K(I) = 110 +/- 10 and 100 +/- 10 nm, respectively). When LN-1-255 inactivated SHV beta-lactamases, a single intermediate was detected by mass spectrometry. The crystal structure of LN-1-255 in complex with SHV-1 was determined at 1.55A resolution. Interestingly, this novel inhibitor forms a bicyclic aromatic intermediate with its carbonyl oxygen pointing out of the oxyanion hole and forming hydrogen bonds with Lys-234 and Ser-130 in the active site. Electron density for the "tail" of LN-1-255 is less ordered and modeled in two conformations. Both conformations have the LN-1-255 carboxyl group interacting with Arg-244, yet the remaining tails of the two conformations diverge. The observed presence of the bicyclic aromatic intermediate with its carbonyl oxygen positioned outside of the oxyanion hole provides a rationale for the stability of this inhibitory intermediate. The 2'-substituted penicillin sulfone, LN-1-255, is proving to be an important lead compound for novel beta-lactamase inhibitor design.

Selected figure(s)

Figure 1.
Chemical structures of the β-lactamase inhibitors. A, general structure of 7-alkylidene-3-substituted cephalosporin sulfones. B, general structure of 6-alkylidene-2′-substituted penicillin sulfones. C, LN-1-255. D, tazobactam sodium.

Figure 8.
Proposed mechanism of enzymatic inhibition by the 6-(pyridylmethylidene)penicillin sulfone series of inhibitors.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2009, 284, 945-953) copyright 2009.

Figures were selected by an automated process.